Tagged with #trimming
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Created 2015-10-21 08:15:13 | Updated | Tags: picard trimming readadaptortrimmer

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Is there a "Best Practices" for how to use ReadAdaptorTrimmer? To me it seems that there is a Catch 22, if one wants to use GATK and Picard.

According to the ReadAdaptorTrimmer documentation: "Read data MUST be in query name ordering as produced, for example with Picard's FastqToBam". Therefore, I would start by doing

java picard.jar FastqToSam FASTQ={r1_file} FASTQ2={r2_file} OUTPUT={bam_file} SM={sample} SORT_ORDER=queryname

to convert my FASTQ files into a sorted uBAM file. However, ReadAdaptorTrimmer requires the BAM file to be indexed, but if I then try

java picard.jar BuildBamIndex INPUT={bam_file}

it fails because BuildBamIndex requires that the BAM file is sorted by coordinate (which does not make sense since the reads are not yet aligned).

Thanks, Michael

Created 2013-11-26 01:16:34 | Updated | Tags: mutect trimming

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GATK 2.7 does not require quality trimming anymore as the tools take base qualities into account. Is it OK to use these untrimmed reads with Mutect as well? Should I expect a big difference comparing the Mutect calls of trimmed and untrimmed versions of the raw reads?

Created 2013-07-15 15:02:11 | Updated | Tags: exome trimming

Comments (7)


Sorry if this is the wrong forum for this question - I just thought someone might have an idea/opinion...

Should I trim/filter exome sequencing reads prior to mapping with BWA and variant calling using GATK? I am currently filtering out reads in which <80% of bases have quality>=Q30 but I lose >20% of my reads this way. Does GATK take quality into account therefore rendering pre-mapping filtering unecessary?

Thanks in advance, Kath